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- PDB-2w4s: novel RNA-binding domain in Cryptosporidium parvum at 2.5 angstro... -

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Basic information

Entry
Database: PDB / ID: 2w4s
Titlenovel RNA-binding domain in Cryptosporidium parvum at 2.5 angstrom resolution
ComponentsAnkyrin-repeat protein
KeywordsSTRUCTURAL PROTEIN / RNA TRANSPORT
Function / homologyPHAX RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Ankyrin-repeat protein
Function and homology information
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsVarrot, A. / Mackereth, C. / Mourao, A. / Sattler, M. / Cusack, S.
CitationJournal: RNA / Year: 2010
Title: Structure and RNA Recognition by the Snrna and Snorna Transport Factor Phax.
Authors: Mourao, A. / Varrot, A. / Mackereth, C. / Cusack, S. / Sattler, M.
History
DepositionDec 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin-repeat protein
B: Ankyrin-repeat protein
C: Ankyrin-repeat protein
D: Ankyrin-repeat protein


Theoretical massNumber of molelcules
Total (without water)52,0284
Polymers52,0284
Non-polymers00
Water1,65792
1
C: Ankyrin-repeat protein
D: Ankyrin-repeat protein


Theoretical massNumber of molelcules
Total (without water)26,0142
Polymers26,0142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-14.1 kcal/mol
Surface area9870 Å2
MethodPISA
2
A: Ankyrin-repeat protein
B: Ankyrin-repeat protein


Theoretical massNumber of molelcules
Total (without water)26,0142
Polymers26,0142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13.9 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 52.862, 99.315
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA388 - 4755 - 92
21THRTHRCC388 - 4755 - 92
12METMETBB389 - 4756 - 92
22METMETDD389 - 4756 - 92

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.989, 0.019, -0.143), (-0.018, -1, -0.014), (-0.144, -0.011, 0.99)
Vector: 1.00148, 1.11596, -0.46691)

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Components

#1: Protein
Ankyrin-repeat protein


Mass: 13007.067 Da / Num. of mol.: 4 / Fragment: RNA-BINDING DOMAIN, RESIDUES 387-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: IOWA / Gene: 1MB.655 / Plasmid: PROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ORIGAMI / References: UniProt: A0A7G2HK26
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.13 %
Description: PHASES WERE OBTAINED BY MAD WITH SELENOMETHIONYL SUBSTITUTED PROTEIN AND A PARTIAL MODEL WAS BUILD.
Crystal growpH: 5.5 / Details: 1.2M NA/K TARTRATE, 100 MM BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 14569 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIAL MODEL IN ANOTHER SPACE GROUP

Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 17.557 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.476 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 769 5 %RANDOM
Rwork0.193 ---
obs0.196 14569 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.45 Å2
2--0.68 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 0 92 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9673774
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.27224.961127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54815567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7761520
X-RAY DIFFRACTIONr_chiral_restr0.1310.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022000
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21311
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21972
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.51772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27122782
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93331165
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2444.5992
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A694loose positional0.55
12C694loose positional0.55
21B678loose positional0.445
22D678loose positional0.445
11A694loose thermal1.8410
12C694loose thermal1.8410
21B678loose thermal1.6810
22D678loose thermal1.6810
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 49
Rwork0.208 743
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
22.7923-0.78320.27973.22351.50264.5415-0.03720.29920.1344-0.3346-0.1430.0727-0.277-0.52280.18020.05910.0205-0.0324-0.093-0.0207-0.18116.68127.4136.69
32.91981.12551.11182.8867-0.37845.46230.0627-0.05210.17430.0583-0.25610.0016-0.38880.13470.1934-0.00210.05720.0301-0.04250.0373-0.212318.33923.545109.636
42.678-1.0840.04644.793-2.53153.95360.0940.1547-0.1364-0.1938-0.4391-0.25470.20070.90160.34510.05970.08770.06390.16920.129-0.132227.00930.21888.018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2B388 - 475
2X-RAY DIFFRACTION3C388 - 475
3X-RAY DIFFRACTION4D388 - 475

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